Technical Abstract:
At an arguable date of around 330,000 years ago there were already at least two different types of cattle that became ancestors of nearly all modern cattle, the Bos primigenius taurus more adapted to temperate climates and the tropically adapted Bos primigenius indicus. Human selection exponentially intensified these differences, especially after the introduction of the concept of breed type. To better detect genomic regions between these subspecies, animals from the International Bovine HapMap were genotyped for over 750,000 SNP across the genome and compared using smoothed FST. The taurine sample was represented by ten breeds and the contrasting zebu cohort by three breeds. Each cattle group evidenced similar numbers of polymorphic markers well distributed across the genome. Principal component analyses and unsupervised hierarchical clustering confirmed the well characterized main division between these subspecies of domestic cattle. The top 1% smoothed FST, associated to positive selection contained 48 genomic regions across 17 chromosomes. Amongst the strongest signals were the BTA7:~50Mb and BTA14:~25Mb; both regions harboring candidate genes and very different patterns of linkage disequilibrium that potentially represent intrinsic differences between cattle types. Nearly half of the top FST signals (n=22) were previously detected using a lower density SNP assay. The bottom 1% of the smoothed FST values included 24 regions across 13 chromosomes, which are potentially associated to balancing selection. These regions often overlap with copy number variants, including the highly variable region at BTA23:~24Mb that harbors a large number of MHC genes. Under these regions, 318 unique Ensembl genes are annotated; many of which are linked to immune response resulting in a significant overrepresentation of immune related pathways. Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified. These regions are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.